From 863e95be861be1bd65c1812fec6e5972e209da73 Mon Sep 17 00:00:00 2001
From: nservant <nicolas.servant@curie.fr>
Date: Fri, 6 May 2022 17:36:31 +0200
Subject: [PATCH] [MODIF] deal with technical replicates
---
workflows/hic.nf | 27 ++++++++++++++++++++++++---
1 file changed, 24 insertions(+), 3 deletions(-)
diff --git a/workflows/hic.nf b/workflows/hic.nf
index 4592e83..f66e16d 100644
--- a/workflows/hic.nf
+++ b/workflows/hic.nf
@@ -143,6 +143,16 @@ Channel.fromPath( params.fasta )
// Info required for completion email and summary
def multiqc_report = []
+def setMetaChunk(row){
+ def map = []
+ row[1].eachWithIndex() { file,i ->
+ meta = row[0].clone()
+ meta.chunks = i
+ map += [meta, file]
+ }
+ return map
+}
+
workflow HIC {
ch_versions = Channel.empty()
@@ -153,8 +163,19 @@ workflow HIC {
INPUT_CHECK (
ch_input
)
+ .reads
+ .map {
+ meta, fastq ->
+ meta.id = meta.id.split('_')[0..-2].join('_')
+ [ meta, fastq ] }
+ .groupTuple(by: [0])
+ .flatMap { it -> setMetaChunk(it) }
+ .collate(2)
+ .set { ch_fastq }
+
+ ch_fastq.view()
- INPUT_CHECK.out.reads.view()
+ //INPUT_CHECK.out.reads.view()
//
// SUBWORKFLOW: Prepare genome annotation
@@ -169,7 +190,7 @@ workflow HIC {
// MODULE: Run FastQC
//
FASTQC (
- INPUT_CHECK.out.reads
+ ch_fastq
)
ch_versions = ch_versions.mix(FASTQC.out.versions)
@@ -177,7 +198,7 @@ workflow HIC {
// SUB-WORFLOW: HiC-Pro
//
HICPRO (
- INPUT_CHECK.out.reads,
+ ch_fastq,
PREPARE_GENOME.out.index,
PREPARE_GENOME.out.res_frag,
PREPARE_GENOME.out.chromosome_size,
--
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